1QY2

Thermodynamics of Binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the Major Urinary Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Thermodynamics of Binding of 2-Methoxy-3-isopropylpyrazine and 2-Methoxy-3-isobutylpyrazine to the Major Urinary Protein.

Bingham, R.J.Findlay, J.B.C.Hsieh, S.-Y.Kalverda, A.P.Kjellberg, A.Perazzolo, C.Phillips, S.E.V.Seshadri, K.Trinh, C.H.Turnbull, W.B.Bodenhausen, G.Homans, S.W.

(2004) J.Am.Chem.Soc. 126: 1675-1681

  • DOI: 10.1021/ja038461i
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the present study we examine the thermodynamics of binding of two related pyrazine-derived ligands to the major urinary protein, MUP-I, using a combination of isothermal titration calorimetry (ITC), X-ray crystallography, and NMR backbone (15)N an ...

    In the present study we examine the thermodynamics of binding of two related pyrazine-derived ligands to the major urinary protein, MUP-I, using a combination of isothermal titration calorimetry (ITC), X-ray crystallography, and NMR backbone (15)N and methyl side-chain (2)H relaxation measurements. Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than the classical entropy-driven hydrophobic effect. Unfavorable entropic contributions from the protein backbone and side-chain residues in the vicinity of the binding pocket are partially offset by favorable entropic contributions at adjacent positions, suggesting a "conformational relay" mechanism whereby increased rigidity of residues on ligand binding are accompanied by increased conformational freedom of side chains in adjacent positions. The principal driving force governing ligand affinity and specificity can be attributed to solvent-driven enthalpic effects from desolvation of the protein binding pocket.


    Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, School of Biochemistry & Molecular Biology, University of Leeds, LS2 9JT Leeds, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major Urinary Protein
A
174Mus musculusMutation(s): 0 
Gene Names: Mup2
Find proteins for P11589 (Mus musculus)
Go to UniProtKB:  P11589
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
IPZ
Query on IPZ

Download SDF File 
Download CCD File 
A
2-ISOPROPYL-3-METHOXYPYRAZINE
2-METHOXY-3-ISOPROPYLPYRAZINE
C8 H12 N2 O
NTOPKICPEQUPPH-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IPZΔG: -17.2 - -33.9 kJ/mol (98) BINDINGDB
IPZKd: 1800 nM BINDINGMOAD
IPZKd: 1800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 53.248α = 90.00
b = 53.248β = 90.00
c = 137.703γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
CCP4data scaling
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance